Merge pull request #6 from ajz34/legacy

Legacy pyxdh update

.github/workflows/pypadeploy.yml

@@ -0,0 +1,25 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -10,6 +10,9 @@ release
 *.chk
 *.bak
 *.sav
+.idea/
+*.iml
+*.xml
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "docs/source/MathJax"]
-	path = docs/source/_static/Mathjax
-	url = https://github.com/mathjax/MathJax.git

.readthedocs.yml → .readthedocs.yaml

@@ -2,17 +2,17 @@ version: 2
 
 sphinx:
   configuration: docs/source/conf.py
-
-submodules:
-  include: all
+  builder: html
 
 build:
-  image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  apt_packages:
+    - pandoc
 
 python:
-  version: 3.7
   install:
     - requirements: docs/requirements.yml
-  system_packages: true
 
 formats: [htmlzip]

Dockerfile

@@ -1,10 +1,10 @@
 # https://hub.docker.com/r/jupyter/base-notebook/dockerfile
 
-FROM python:3.7-slim
+FROM python:3.8-slim
 
 ENV DEBIAN_FRONTEND noninteractive
 RUN apt-get update && apt-get -yq dist-upgrade && \
-    apt-get install -yq --no-install-recommends git && \
+    apt-get install -yq --no-install-recommends git gcc && \
     rm -rf /var/lib/apt/lists/*
 
 ENV WRK_DIR "/work"
@@ -13,28 +13,15 @@ ENV PKG_DIR="$WRK_DIR/pyxdh"
 RUN mkdir $WRK_DIR
 WORKDIR $WRK_DIR
 
-RUN mkdir -p $PKG_DIR && \
-    git clone https://github.com/ajz34/Py_xDH.git $PKG_DIR && \
-    cp $PKG_DIR/.pyscf_conf.py ~/.pyscf_conf.py
+RUN mkdir -p $PKG_DIR
+RUN git clone https://github.com/ajz34/Py_xDH.git $PKG_DIR
+# RUN cd $PKG_DIR/ && git checkout --force origin/legacy
+RUN cp $PKG_DIR/.pyscf_conf.py ~/.pyscf_conf.py
 
 RUN pip --no-cache-dir install -r $PKG_DIR/requirements.txt
-RUN pip --no-cache-dir install -r $PKG_DIR/docs/requirements.yml
-RUN pip --no-cache-dir install jupyter_contrib_nbextensions
-RUN jupyter contrib nbextension install
-RUN for extension in \
-        nbextensions_configurator/config_menu/main \
-        hide_input/main \
-        scratchpad/main \
-        collapsible_headings/main \
-        toc2/main \
-        nbextensions_configurator/tree_tab/main \
-        codefolding/edit \
-        jupyter-js-widgets/extension; \
-    do jupyter nbextension enable $extension --sys-prefix; done
-RUN mkdir -p ~/.jupyter/custom && \
-    echo ".container { width:85%; }" > ~/.jupyter/custom/custom.css
 
 ENV PYTHONPATH $PKG_DIR:$PYTHONPATH
+ENV OMP_NUM_THREADS=4
 
 EXPOSE 8888
 

README.md

@@ -1,8 +1,8 @@
 # Python xDH Project
 
-**This project is under going code refactorization. Document code is currently not updated. Unrestricted and RI implementation is on-going.**
+**This project is under going code refactorization. Document code is currently not updated. Unrestricted and RI implementation is on-going. Also refers to unfinished [dh project](https://github.com/ajz34/pyscf-forge/tree/pre-0.2).**
 
-**程序正在进行重构。其所对应的文档目前还没有更新。开窍层与 RI 实现目前还有待完善。**
+**程序正在进行重构。其所对应的文档目前还没有更新。开壳层与 RI 实现目前还有待完善。同时参见尚未完成的 [dh 项目](https://github.com/ajz34/pyscf-forge/tree/pre-0.2)。**
 
 |         | Badges   |
 | :------ | :------- |
@@ -39,7 +39,7 @@ basis processing, DFT grid engine and CP-HF algorithm is based on python quantum
 
 ## Version Information
 
-Current version of pyxdh is 0.0.4. This version should work with pyscf==1.7.1.
+Current version of pyxdh is 0.0.7. This version should work with pyscf==1.7.5.
 
 Previous version 0.0.3 should work with pyscf==1.6.4.
 
@@ -133,10 +133,6 @@ print(- polar_xDH.E_2)
 
 ## Documentation
 
-**Note: Documentation remains to be updated! Only `pyxdh` code can be used currently.**
-
-**注意：文档部分仍有待完善！目前为止，`pyxdh` 库的代码确实是可以使用的，但一些文档的代码是有问题的。**
-
 Published web page: https://py-xdh.readthedocs.io/zh_CN/latest/
 
 Prerequisite knowledge of chapter 3, 4, 10 of *A New Dimension to Quantum Chemistry: Analytic Derivative Methods in
@@ -169,10 +165,19 @@ package in terminal successfully.
 
 ## `pyxdh` Package
 
-This is merely a demo package that implements derivative of some basic quantum chemistry methods.
-Currently it is not distrubuted to PyPI.
+This is merely a demo package that implements derivative of some basic quantum chemistry methods. Not for real-world problem computation, and not efficient at all.
+
+这个库目前只是一个短小的、包含基础量化方法梯度实现的库。它不适合用于实际生产环境的计算；它的效率及其糟糕。
+
+### Installation
+
+Currently, PyPI installation is available. Python version 3.8 should work.
 
-这个库目前只是一个短小的、包含基础量化方法梯度实现的库。它并没有发布到 PyPI 中。
+```bash
+pip install pyxdh
+```
+
+See also [docker image](#Docker-Image).
 
 ### Deficiencies and facilities
 
@@ -267,6 +272,9 @@ Simply follow the instructions from terminal should work.
 - Thanks labmates for valuable discussions and suggestions.
 - Thanks supervisor and teachers in lab for project support and server support.
 - Thanks parents for project support.
-- Currently, the author does not know any funding grants supporting this project. It should have some.
-  Project is almost personally driven at this stage.
 - Futher discussion is welcomed by raising issue or e-mail. Chinese is prefered; English is also okay.
+- Funding information: National Natural Science Foundation of China (Grant 21688102), the Science Challenge Project (Grant TZ2018004), and the National Key Research and Development Program of China (Grant 2018YFA0208600).
+
+This project is not going to be formally published, as it is more like documentation demo instead of program. This project is closely related to the following article:
+> Gu, Y.; Zhu, Z.; Xu, X. Second-Order Analytic Derivatives for XYG3 Type of Doubly Hybrid Density Functionals: Theory, Implementation, and Application to Harmonic and Anharmonic Vibrational Frequency Calculations. J. Chem. Theory Comput. 2021, 17 (8), 4860–4871. https://doi.org/10.1021/acs.jctc.1c00457.
+

docs/requirements.yml

@@ -1,9 +1,9 @@
-numpy!=1.16
+numpy
 scipy
 jupyter
 matplotlib
 sphinx
 nbsphinx
-nbconvert!=5.4
+nbconvert
 sphinx_rtd_theme
 sphinxcontrib-bibtex

docs/source/conf.py

@@ -171,7 +171,7 @@
 
 nbsphinx_allow_errors = True
 nbsphinx_timeout = 720
-mathjax_path = "Mathjax/es5/tex-chtml-full.js"
+mathjax_path = "https://lf26-cdn-tos.bytecdntp.com/cdn/mathjax/3.2.0/es5/tex-chtml-full.js"
 
 bibtex_bibfiles = [
     "qcbasic/basic_gga.bib",
@@ -180,5 +180,5 @@
     "qcbasic/basic_rhf.bib",
     "qcbasic/basic_b2plyp.bib",
     "qcbasic/basic_xyg3.bib",
-    "ref.bib",
+    # "ref.bib",
 ]

pyproject.toml

@@ -0,0 +1,48 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyxdh"
+version = "v0.0.7"
+authors = [
+    {name = "ajz34", email = "ajz34@outlook.com"},
+]
+description = "Document and code of python and PySCF approach XYG3 type of density functional realization"
+readme = "README.md"
+requires-python = ">=3.8, <3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: POSIX :: Linux",
+]
+dependencies = [
+    "pyscf==1.7.5",
+    "h5py==3.0",
+    "scipy==1.4.1",
+    "numpy==1.18",
+    "opt_einsum",
+    "jupyter",
+    "sphinx",
+    "nbsphinx",
+    "pyberny",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-bibtex",
+    "jupyter_contrib_nbextensions",
+    "pandoc",
+    "matplotlib",
+    "docopt",
+    "codecov",
+    "pytest-cov",
+]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+"pyxdh.Validation.numerical_deriv" = ["*.dat"]
+"pyxdh.Validation.gaussian" = ["*.fchk"]
+
+[project.urls]
+Homepage = "https://github.com/ajz34/Py_xDH"
+Documentation = "https://py-xdh.rtfd.io"

requirements.txt

@@ -1,7 +1,8 @@
-pyscf>=1.7.1
-numpy!=1.16
+pyscf==1.7.5
+h5py==3.0
+scipy==1.4.1
+numpy==1.18
 opt_einsum
-scipy
 jupyter
 sphinx
 nbsphinx
@@ -10,6 +11,7 @@ sphinx_rtd_theme
 sphinxcontrib-bibtex
 jupyter_contrib_nbextensions
 pandoc
+matplotlib
 docopt
 codecov
 pytest-cov